I am planning to use 2 RTL-SDR dongles on a single computer. The thing is, they will be operating on 2 different frequencies, and so different antennas will be used.

I would like one instance of rtl_fm or gnuradio to open set to "frequency 1" and connect to a specific USB port. Then the other instance on "frequency 2" to another USB port.

I know that in Linux, USB ports are defined at a kernel level as such:
"The name given to this device by the kernel (KERNELS=="1-4.5") indicates that this device is plugged into the fifth port of a hub connected to port four on bus 1"

The computer I am using has no hub, and only one bus. It has 4 ports. So I would like to use 1-3.1 and 1-4.1 for example.

Kap, not a problem. If your using linux, you won't be working with usb port assignment #'s.
You'll use rtl_test. It will tell you what device each dongle is in which will be enumerated as -d 0, -d 1 , -d 2
etc...you'll use these # in gnuradio and the other apps....as in rtl=0 ....rtl =1 ...or depending on the app -d 0, -d 1, -d 2
I use Ubuntu.....the last dongle plugged in seems to always take -d 0, and bump everyone down one.